The aim of this study was to determine the natural occurrence of Nosema apis in honey bee colonies and evaluated of N. apis presence in colonies after medical treatment with fumagillin and thymol in consecutive 3 years period. For this purpose, 208 honey bee colonies randomly selected for detection of N. apis infection from Aegean ecotype of Apis mellifera anatolica, one year old queen in April 2002. The colony development performances and honey yields were evaluated through the years from 2002 to 2004. Infested colonies were classified in 3 groups as tried to be equalized in Nosema infestation level; Fumidil-B, thymol application and control (only sugar syrup feeding). The effects of using period of Fumidil-B, contains fumagillin and thymol on N. apis infected honeybee colonies were researched by determining winter losses, adult bees population, brood and honey production in consecutive years. Also, control group were impacted for same parameters. The adult bee worker population and brood surfaces of treated in both groups (Fumidil-B and thymol) were increased significantly (p<0.05) by years from 2002 to 2004. Honey production of thymol group was exhibited significant (p<0.05) increase by years, consequently. Significant decrease (p<0.05) was recorded in control group for winter mortality, brood production, adult bee worker population and honey yield than the other treatment groups. The study was conducted that, observations of bee hives and regular treatment of infested colonies supported healthy and more productive honey bees. Leaving colonies un-medicated caused severe problems in colony production. Thymol could be suggested to beekeeper as a qualified Nosemiasis prevent agent; cheap, practical and non-toxic in hives for organic honey production. Moreover, with using thymol, residue-free bee products could be handled economically.